4F8L

X-ray structure of PsaA from Yersinia pestis, in complex with galactose and AEBSF

• PDB DOI:  https://doi.org/10.2210/pdb4F8L/pdb

• Classification: CELL ADHESION/inhibitor
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-17 Released: 2013-05-22 
• Deposition Author(s): Bao, R., Esser, L., Xia, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.182 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

Literature

Structural basis for the specific recognition of dual receptors by the homopolymeric pH 6 antigen (Psa) fimbriae of Yersinia pestis.

Bao, R., Nair, M.K., Tang, W.K., Esser, L., Sadhukhan, A., Holland, R.L., Xia, D., Schifferli, D.M.

(2013) Proc Natl Acad Sci U S A 110: 1065-1070

• PubMed: 23277582 
• DOI: https://doi.org/10.1073/pnas.1212431110
• Primary Citation of Related Structures:  
  4F8L, 4F8N, 4F8O, 4F8P


• PubMed Abstract: 
  

The pH 6 antigen (Psa) of Yersinia pestis consists of fimbriae that bind to two receptors: β1-linked galactosyl residues in glycosphingolipids and the phosphocholine group in phospholipids. Despite the ubiquitous presence of either moiety on the surface of many mammalian cells, Y. pestis appears to prefer interacting with certain types of human cells, such as macrophages and alveolar epithelial cells of the lung. The molecular mechanism of this apparent selectivity is not clear. Site-directed mutagenesis of the consensus choline-binding motif in the sequence of PsaA, the subunit of the Psa fimbrial homopolymer, identified residues that abolish galactosylceramide binding, phosphatidylcholine binding, or both. The crystal structure of PsaA in complex with both galactose and phosphocholine reveals separate receptor binding sites that share a common structural motif, thus suggesting a potential interaction between the two sites. Mutagenesis of this shared structural motif identified Tyr126, which is part of the choline-binding consensus sequence but is found in direct contact with the galactose in the structure of PsaA, important for both receptor binding. Thus, this structure depicts a fimbrial subunit that forms a polymeric adhesin with a unique arrangement of dual receptor binding sites. These findings move the field forward by providing insights into unique types of multiple receptor-ligand interactions and should steer research into the synthesis of dual receptor inhibitor molecules to slow down the rapid progression of plague.

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Organizational Affiliation: 

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.75 kDa 
• Atom Count: 1,320 
• Modelled Residue Count: 138 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pH 6 antigen	A	145	Yersinia pestis	Mutation(s): 0  Gene Names: psaA, y2882, YPO1303, YP_1289
UniProt
Find proteins for P31522 (Yersinia pestis) Explore P31522  Go to UniProtKB:  P31522

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AES	NA [auth A]	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE C8 H10 F N O2 S MGSKVZWGBWPBTF-UHFFFAOYSA-N
GAL	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
MLI	PA [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
BR	AA [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
GLY	OA [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
GAI	JA [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	Binding MOAD:  4F8L	IC50: 4.00e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.182 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.108	α = 90
b = 54.164	β = 90
c = 101.626	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Bao, R., Esser, L., Xia, D.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary